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Correlation of mitochondrial composition with SARS-CoV-2 reads for individual species

Each panel shows the correlation across all samples between the percent of all high-quality (preprocessed) reads that align to SARS-CoV-2 versus the percent that align to the mitochondrial genomes for the indicated species. The orange numbers give the Pearson correlation coefficient.

You can select which species to show using the dropdown at the bottom of the plot.

Other options at the bottom enable:

• selection of samples only from specific collection dates (click on circles next to select)
• only samples collected from particular sources
• whether the percent mitochondrial reads is computed as the percent of all high-quality (preprocessed) reads or as the percent of reads that align to mitochondrial genomes from any species
• whether the axis scales show the raw percentages of the log10 of the percentages; when using a log scale percentages of zero are set to half the lowest observed percentage across all samples and species
• selection of samples only with a sufficient number of total aligned mitochondrial reads

Mouseover points for details on particular samples.

The correlation coefficients will change accordingly if you select different options for how the percent mitochondrial reads is computed or whether we analyze the direct or log10 percents.

See https://github.com/jbloom/Huanan_market_samples for results files and a fully reproducible computational pipeline.

See https://jbloom.github.io/Huanan_market_samples for links to all interactive plots.